It uses try_seq function repeatedly trying to positioned each marker
in a vector of markers into a already ordered sequence.
Each marker in the vector "markers" is kept in the sequence
if the difference of LOD and total group size of the models
with and without the marker are below the thresholds "lod.thr" and "cM.thr".
try_seq_by_seq(sequence, markers, cM.thr = 10, lod.thr = -10, verbose = TRUE)An object of class sequence, which is a list containing the
following components:
a vector containing the
(ordered) indices of markers in the sequence, according to the input file.
a vector with the linkage phases between markers
in the sequence, in corresponding positions. -1 means that there are
no defined linkage phases.
a vector with the
recombination frequencies between markers in the sequence. -1 means
that there are no estimated recombination frequencies.
log-likelihood of the corresponding linkage map.
name of the object of class onemap with the raw
data.
name of the object of class rf_2pts with the
2-point analyses.
object of class sequence with ordered markers
vector of integers defining the marker numbers to be inserted in the sequence
number defining the threshold for total map size increase when inserting a single marker
the difference of LODs between model before and after inserting the marker need to have value higher than the value defined in this argument
A logical, if TRUE it output progress status information.